XΥMTEX (Version 4.05) for Typesetting Chemical Structural Formulas: A. Lewis Structures Drawn by the Lewisstruc Package

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XΥMTEX (Version 4.05) for Typesetting Chemical Structural Formulas: A. Lewis Structures Drawn by the lewisstruc Package.

Shinsaku Fujita

Shonan Institute of Chemoinformatics and Mathematical Chemistry Kaneko 479-7 Ooimachi, Ashigara-Kami-Gun, Kanagawa, 258-0019 Japan

November 25, 2009 (For Version 4.05) c

Contents

1 Introduction 5 1.1History...... 5 1.2 Use of the lewisstruc Package...... 6 1.3 Recent Books Citing the XΥMTEXSystem...... 6 2 Lone Pairs and Radicals 7 2.1BasicCommandsforDrawingLonePairs...... 7 2.2BasicCommandsforDrawingRadicals...... 9 2.3LewisStructures...... 11 2.3.1 AtomswithanAtomthroughaLonePair...... 11 2.3.2 TetrahedralLewisStructures...... 12 2.3.3 NestedTetrahedralLewisStructures...... 15 2.4 Additional Examples for Compounds with Lone Pairs ...... 18 3 Chemical Schemes with Lewis Structures 21 3.1ResonanceForms...... 21 3.2RadicalFissions...... 24 3.3Carbocations...... 25 3.4 Nucleophilic Substitutions of Order Two ...... 26 3.5Carboanions...... 27 3.6 Aromatic Nucleophilic Substitutions ...... 28 3.7FurtherReactions...... 30 3.7.1 FormationandReactionsofDiazoketones...... 30 3.7.2 Williamson Ether Synthesis ...... 32

Chapter 1

Introduction

1.1 History

The history of the XΥMTEX system is summarized in Table 1.1:

Table 1.1: Versions of XΥMTEX version package ﬁles and comments 1.00 (1993) (for LATEX2.09) See Ref. [1, 2]. aliphat.sty, carom.sty, lowcycle.sty, hetarom.sty, hetaromh.sty, hcycle.sty, chemstr.sty, locant.sty, xymtex.sty 1.01 (1996) (for LATEX2ε) See Ref. [3]. ccycle.sty, polymers.sty, chemist.sty 1.02 (1998) (not released) Nested substitution by ‘yl’-function. 2.00 (1998) Enhanced version based on the XΥM Notation. See Ref. [4, 5]. fusering.sty, methylen.sty 2.01 (2001) (not released) Size reduction, sizeredc.sty (version 1.00) 3.00 (2002) Size reduction (sizeredc.sty, version 1.01), and reconstruction of the command system. See Ref. [6] 4.00 (2002) (not released) PostScript printing (xymtx-ps.sty, version 1.00 and chmst-ps.sty, version 1.00) 4.01 (2004) PostScript printing and length-variable central atoms [7] 4.02 (2004) PostScript printing and wedges bonds for stereochemistry [8] 4.03 (2005) PostScript printing and wavy bonds for stereochemistry [8] 4.04 (2009) Macros for drawing steroids (steroid.sty, ver 1.00) [9] 4.05 (2009) (The present version) New macros for drawing Lewis structures of the lewissturc package (lewisstruc.sty, version 1.00), revised and improved macros added to the chemist package (ver 4.05) [and the chmst-ps package (ver 1.02)], and the ﬁrst release of the chemtimes package (ver 1.00)

Among the new matters of the XΥMTEX system (version 4.05) summarized in Table 1.1, this manual is concerned with macros for drawing Lewis structures of the lewissturc package (lewisstruc.sty, version 1.00).

5 6 FUJITA Shinsaku: XΥMTEX 1.2 Use of the lewisstruc Package

Because the lewisstruc package is part of the XΥMTEX system, it is automatically loaded when the XΥMTEX system is loaded by declaring Yusepackage{xymtexps} (POSTSCRIPT-compatible mode) or Yusepackage {xymtex} (TEX/LATEX mode) in the preamble of a document to be typeset. The following template shows a typical description for loading the XΥMTEX system including the lewisstruc package. %Test405A.tex Ydocumentclass{article} Yusepackage{xymtexps}%loading the XyMTeX system (involving lewisstruc.sty) Yusepackage{chemist,chmst-ps}%loading of the chemist package (not requisite) Ybegin{document} (text) Yend{document}

The tex ﬁle named Test405A.tex (stored in the c:Yfujita directory for example) is processed by LATEX2ε, where the following command is input in a command line (e.g., in the command-prompt window of Windows XP).

c>Yfujita latex Test405A

The resulting DVI ﬁle (Test405A.dvi) is then converted into a POSTSCRIPT ﬁle by using dvips(k):

c>Yfujita dvipsk -D2400 -Pdl Test405A

Thereby, you are able to obtain Test405.ps as a POSTSCRIPT file, which can be browsed by means of GSview/GhostScript. Alternatively, the POSTSCRIPT file (Test405.ps) is further converted into a PDF file by using Adobe Distiller. The resulting PDF file (Test405.pdf) can be browsed by Adobe Reader.

Note: This document uses the Y symbol to show each control sequence according to Japanese encoding. For example, the above template is transformed into the one with non-Japanese encoding, as follows:

%Test405A.tex \documentclass{article} \usepackage{xymtexps}%loading the XyMTeX system (involving lewisstruc.sty) \usepackage{chemist,chmst-ps}%loading of the chemist package (not requisite) \begin{document} (text) \end{document}

1.3 Recent Books Citing the XΥMTEX System

Recent books on LATEX2ε have referred to the XΥMTEX system, e.g., pages 520–540 of [10] and pages 551–598 of Vol. II of [11]. Chapter 2

Lone Pairs and Radicals

2.1 Basic Commands for Drawing Lone Pairs

The command Yoverpair supported by the lewisstruc package (included in the XΥMTEXsystem)draws a lone pair over an atom speciﬁed by its argument, while the command Yunderpair draws a lone pair under an atom speciﬁed by its argument. They can be nested freely, as follows:

single usage: Yoverpair{O} Yunderpair{N} Yqquad nested usage: Yunderpair{Yoverpair{O}} Yoverpair{Yunderpair{N}} ...... single usage: ON.. nested usage: O.. N.. The YLewisSbond command draws a lone pair in the form of a semicolon. The Lewis structures of hydrogen ﬂuoride and water are typeset as follows: HF Yqquad HYLewisSbondYoverpair{Yunderpair{F}}YLewisSbond{} Yqquad HYsbondYoverpair{Yunderpair{F}}YLewisSbond{} YY[5pt] Ychemform{H_{2}O} Yqquad HYLewisSbondYoverpair{Yunderpair{O}}YLewisSbond{}H Yqquad HYsbondYoverpair{Yunderpair{O}}Ysbond{}H ...... HF H.F... H F...... H2OH.O...HHO.. H The command YlonepairA is capable of drawing at most four lone pairs, the positions of which are speciﬁed by its optional argument. The numbering of the four lone pairs is shown as follows: 1 .... 4 .O... 2 3 where a set of numbers for drawing lone pairs (e.g., 124 etc. in an ascending order) is given as an optional argument. A list of such modes of numbering is summarized in the following example: YlonepairA{O} Yqquad YlonepairA[1234]{O} Yqquad YlonepairA[123]{O} Yqquad YlonepairA[124]{O} Yqquad YlonepairA[134]{O} Yqquad YlonepairA[234]{O} YY[5pt] YlonepairA[12]{O} Yqquad YlonepairA[13]{O} Yqquad YlonepairA[14]{O} Yqquad YlonepairA[23]{O} Yqquad YlonepairA[24]{O} Yqquad YlonepairA[34]{O} YY[5pt] YlonepairA[1]{O} YqquadYlonepairA[2]{O} Yqquad YlonepairA[3]{O} Yqquad YlonepairA[4]{O} Yqquad YlonepairA[5]{O}

7 8 FUJITA Shinsaku: XΥMTEX

...... O... .O... O... .O. .O.. .O...... O. O.. .OO... .O. .O...... OO. O.. .O .O...

An element represented by two alphabets (e.g., Ne) can be attached by four lone pairs by using the . .. . YlonepairA command. Thus, the command YlonepairA[1234]{Ne} outputs .Ne.. . properly. By using the command YlonepairA, the Lewis structures of hydrogen ﬂuoride and water are alternatively typeset as follows:

HF Yqquad HYLewisSbondYlonepairA[123]{F} Yqquad HYsbondYlonepairA[123]{F} YY[5pt] Ychemform{H_{2}O} Yqquad HYLewisSbondYlonepairA[13]{O}YLewisSbond{}H Yqquad HYsbondYlonepairA[13]{O}Ysbond{}H ...... HF H.F... H F...... H2OH.O...HHO.. H

An atom with lone pairs (drawn by YlonepairA) can be incorporated in a structural formula due to the XΥMTEX system. The following example shows benzene derivatives with hydroxyl substituents, which contain lone pairs by means of YlonepairA.

Ybzdrv[l]{1==YlonepairA[14]{O}H;4==YlonepairA[34]{O}H} Ybzdrv[r]{1==Ylmoiety{HYlonepairA[12]{O}};4==Ylmoiety{HYlonepairA[23]{O}}} Ybzdrv[A]{2==YlonepairA[13]{O}H} Ybzdrv{2==YlonepairA[13]{O}YLewisSbond{}H} .. .. .OH HO...... O..H O...H

. . .O..H HO...

Although lone pairs of heterocyclic compounds are usually abbreviated in organic chemistry, they participate in nucleophilic reactions as neceophiles. To show such participation explicitly, lone pairs are drawn by YlonepairA as follows:

Yfuranv{} Yfiveheterov[bd]{1==YlonepairA[13]{O}}{} Ypyridinev{} Ysixheterov[ace]{1==YlonepairA[1]{N}}{}

.. N N

.. O O.. CHAPTER 2. LONE PAIRS AND RADICALS 9

The command YlonepairB is capable of drawing at most four lone pairs in an alternative mode, where the positions of selected lone pairs are speciﬁed by its optional argument. The numbering of the four lone pairs is shown as follows: 41 ...... O.. 32 where a set of numbers for drawing lone pairs (e.g., 124 etc.) is given as an optional argument. A list of such modes of numbering is summarized in the following example:

YlonepairB{O} Yqquad YlonepairB[1234]{O} Yqquad YlonepairB[123]{O} Yqquad YlonepairB[124]{O} Yqquad YlonepairB[134]{O} Yqquad YlonepairB[234]{O} YY[5pt] YlonepairB[12]{O} Yqquad YlonepairB[13]{O} Yqquad YlonepairB[14]{O} Yqquad YlonepairB[23]{O} Yqquad YlonepairB[24]{O} Yqquad YlonepairB[34]{O} YY[5pt] YlonepairB[1]{O} YqquadYlonepairB[2]{O} Yqquad YlonepairB[3]{O} Yqquad YlonepairB[4]{O} Yqquad YlonepairB[5]{O} ...... O.. ..O.. ..O.. O.. ..O ..O...... O.. ..O O ..O.. O.. ..O ...... O O.. ..O O ..O..

An atom with lone pairs (drawn by YlonepairB) can also be incorporated in a structural formula due to the XΥMTEX system. The following example shows formaldehyde derivatives with a carbonyl oxygen, which contains lone pairs by means of YlonepairB.

YLtrigonal{0==C;1D==YlonepairB[12]{O};2==H;3==H} Yqquad YRtrigonal{0==C;1D==YlonepairB[34]{O};2==H;3==H} Yqquad YUtrigonal{0==C;1D==YlonepairB[23]{O};2==H;3==H} Yqquad YDtrigonal{0==C;1D==YlonepairB[14]{O};2==H;3==H}

.. .. H H O H H .. .. C O.. ..O C C C H H H H ..O..

2.2 Basic Commands for Drawing Radicals

In analogy to the command YlonepairA, the command YchemradicalA is capable of drawing at most four electrons (dots), the positions of which are speciﬁed by its optional argument. The numbering of the four electrons is shown as follows: 1. 4 . . 2 O. 3 where a set of numbers for drawing unpaired electrons (e.g., 124 etc. in an ascending order) is given as an optional argument. A list of such modes of numbering is summarized in the following example:

YchemradicalA{O} Yqquad YchemradicalA[1234]{O} Yqquad YchemradicalA[123]{O} Yqquad YchemradicalA[124]{O} Yqquad YchemradicalA[134]{O} Yqquad YchemradicalA[234]{O} YY[5pt] 10 FUJITA Shinsaku: XΥMTEX

YchemradicalA[12]{O} Yqquad YchemradicalA[13]{O} Yqquad YchemradicalA[14]{O} Yqquad YchemradicalA[23]{O} Yqquad YchemradicalA[24]{O} Yqquad YchemradicalA[34]{O} YY[5pt] YchemradicalA[1]{O} Yqquad YchemradicalA[2]{O} Yqquad YchemradicalA[3]{O} Yqquad YchemradicalA[4]{O} Yqquad YchemradicalA[5]{O} Yqquad ...... O. O. O. O O. O...... O O. OO. O O...... OOO. O O.

A Lewis structure of acetylene is drawn by using the YchemradicalA command.

Ybegin{ChemEquation} YchemradicalA[2]{H} Yquad YchemradicalA[1234]{C} Yquad YchemradicalA[1234]{C} Yquad YchemradicalA[4]{H} Yquad Yrightarrow Yquad HYsbondYchemradicalA[13]{C}YsbondYchemradicalA[13]{C}Ysbond{}H Yquad = Yquad HYsbond{}CYtbond{}CYsbond{}H Yend{ChemEquation} ...... H C. C. H → H C. C. H=H C C H (2.1) Note the ChemEquation environment is supported by the chemist package. In analogy to the command YlonepairB, the command YchemradicalB is capable of drawing at most four electrons (dots), the positions of which are speciﬁed by its optional argument. The numbering of the four electrons is shown as follows: 41. . .O. 32 where a set of numbers for drawing electrons (e.g., 124 etc. in an ascending order) is given as an optional argument. A list of such modes of numbering is summarized in the following example:

YchemradicalB{O} Yqquad YchemradicalB[1234]{O} Yqquad YchemradicalB[123]{O} Yqquad YchemradicalB[124]{O} Yqquad YchemradicalB[134]{O} Yqquad YchemradicalB[234]{O} YY[5pt] YchemradicalB[12]{O} Yqquad YchemradicalB[13]{O} Yqquad YchemradicalB[14]{O} Yqquad YchemradicalB[23]{O} Yqquad YchemradicalB[24]{O} Yqquad YchemradicalB[34]{O} YY[5pt] YchemradicalB[1]{O} Yqquad YchemradicalB[2]{O} Yqquad YchemradicalB[3]{O} Yqquad YchemradicalB[4]{O} Yqquad YchemradicalB[5]{O} Yqquad ...... O. .O. .O. O. .O .O...... O..O O .O. O. .O . . . . O O..O O .O.

A Lewis structure of ethylene is drawn by using the YchemradicalB command, where the ﬁrst structure is drawn by using the picture environment of the native LATEX2ε. Ybegin{ChemEquation} Yraisebox{-18pt}{Yunitlength=0.1pt Ybegin{picture}(425,380)(-103,-171) Yput(-103,171){YchemradicalB[2]{H}} Yput(-103,-171){YchemradicalB[1]{H}} CHAPTER 2. LONE PAIRS AND RADICALS 11

Yput(0,0){YchemradicalB{C}} Yput(200,0){YchemradicalB{C}} Yput(303,171){YchemradicalB[3]{H}} Yput(303,-171){YchemradicalB[4]{H}} Yend{picture}} Yqquad Yrightarrow Yraisebox{-28pt}{% YLtrigonal{0==YchemradicalB[2]{C};2==H;3==H;% 1==YRtrigonal{0==YchemradicalB[3]{C};1==(yl);2==H;3==H}}} YqquadYqquad = Yqquad Yraisebox{-28pt}{Yethylene{}{1==H;2==H;3==H;4==H}} Yend{ChemEquation}

H. .H H H H H . . . . .C. .C. → C. .C = CC (2.2) . . H H H H H H

2.3 Lewis Structures

2.3.1 Atoms with an Atom through a Lone Pair The command Yoverpairover{A}{B} is used to draw an atom (A) attached upward by another atom (B) through a lone pair, while the command Yunderpairunder{A}{B} is used to draw an atom (A) attached downward by another atom (B) through a lone pair. These commands can be nested freely.

--- Yoverpairover{A}{B} Yqquad Yunderpairunder{A}{B} Yqquad Yunderpairunder{Yoverpairover{A}{B}}{X} Yqquad Yoverpairover{Yunderpairunder{A}{B}}{X} ---

B.. B.. X.. — AA.. A.. A.. — B X B Such nested usage of these commands allows us to draw Lewis structures of methane and ammonia, as follows:

HYLewisSbondYunderpairunder{Yoverpairover{C}{H}}{H}YLewisSbond{}H Yqquad HYLewisSbondYoverpairover{Yunderpair{N}}{H}YLewisSbond{}H

H H ...... H.C...HH.N...H H The command Yleftlonepairover{A}{B} is used to draw an atom (A) attached by another atom (B) through a lone pair in the northwest direction, while the command Yrightlonepairover{A}{B} is used to draw an atom (A) attached by another atom (B) through a lone pair in the northeast direction. These commands can be nested freely.

--- Yleftlonepairover{A}{B} Yqquad Yrightlonepairover{A}{B} Yqquad Yrightlonepairover{Yleftlonepairover{A}{B}}{X} Yqquad Yleftlonepairover{Yrightlonepairover{A}{B}}{X} ---

B.. ..BB.. ..XX.. ..B — AAA A — 12 FUJITA Shinsaku: XΥMTEX

Downward counterparts of these commands are also supported by the lewisstruc package. Thus, the command Yleftlonepairunder{A}{B} is used to draw an atom (A) attached by another atom (B) through a lone pair in the southwest direction, while the command Yrightlonepairunder{A}{B} is used to draw an atom (A) attached by another atom (B) through a lone pair in the southeast direction. These commands can be nested freely.

--- Yleftlonepairunder{A}{B} Yqquad Yrightlonepairunder{A}{B} Yqquad Yrightlonepairunder{Yleftlonepairunder{A}{B}}{X} Yqquad Yleftlonepairunder{Yrightlonepairunder{A}{B}}{X} ---

—..AA.. ..A.. ..A..— B BBXX B

These upward-type and downward-type commands can be nested freely, as exempliﬁed by the following outputs:

--- Yrightlonepairunder{Yleftlonepairover{A}{B}}{X} Yqquad Yleftlonepairover{Yleftlonepairunder{A}{B}}{X} Yqquad Yrightlonepairover{Yrightlonepairunder{Yleftlonepairover{A}{B}}{X}}{Y} Yqquad Yleftlonepairunder{Yrightlonepairover{% Yrightlonepairunder{Yleftlonepairover{A}{B}}{X}}{Y}}{Z} ---

B.. X.. B.. ..Y B.. ..Y — A.. ..A A.. ..A..— X B X Z X

2.3.2 Tetrahedral Lewis Structures The command YLewistetrahedralA is capable of drawing at most four atoms through lone pairs, where the positions of selected atoms with lone pairs are speciﬁed by its optional argument. The numbering of the four atoms with lone pairs is shown as follows:

1 .... 4.C...2 3

Following examples show the applicability of the command YLewistetrahedralA.

YLewistetrahedralA{0==C;1==A;2==B;3==X;4==Y} YqquadYqquad YLewistetrahedralA{0==C;1==A;2==B;3==X} YqquadYqquad YLewistetrahedralA{0==C;1==A;2==B;4==X} YqquadYqquad YLewistetrahedralA{0==C;1==A;3==Y;4==X} YqquadYqquad YLewistetrahedralA{0==C;2==B;3==Y;4==X} YY[15pt] YLewistetrahedralA{0==C;1==A;2==B} YqquadYqquad YLewistetrahedralA{0==C;1==A;3==X} YqquadYqquad YLewistetrahedralA{0==C;1==A;4==X} YqquadYqquad YLewistetrahedralA{0==C;2==B;3==X} YqquadYqquad YLewistetrahedralA{0==C;2==B;4==X} YqquadYqquad YLewistetrahedralA{0==C;3==Y;4==X} YY[15pt] YLewistetrahedralA{0==C;1==A} YqquadYqquad YLewistetrahedralA{0==C;2==B} YqquadYqquad YLewistetrahedralA{0==C;3==B} YqquadYqquad YLewistetrahedralA{0==C;4==B} CHAPTER 2. LONE PAIRS AND RADICALS 13

A A A A ...... Y.C...B C...BX.C.BX.C.. X.C...B X X Y Y A A A ...... C.B C.. X.CC...BX.C.BX.C.. X X Y A .. . . CC.BC.. B.C B A Lewis structure of methane is drawn by using the YLewistetrahedralA command. The ﬁrst structure is drawn by using the array environment of the native LATEX2ε,whereYchemradicalA commands are used to draw component radical structures. Ybegin{ChemEquation} Ybegin{array}{ccc} & YchemradicalA[3]{H} & YY[5pt] YchemradicalA[2]{H} & YchemradicalA[1234]{C} & YchemradicalA[4]{H} YY[5pt] & YchemradicalA[1]{H} & YY Yend{array} Yquad Yrightarrow Yquad YLewistetrahedralA{0==C;1==H;2==H;3==H;4==H} Yquad = Yquad Yraisebox{-28pt}{Ytetrahedral{0==C;1==H;2==H;3==H;4==H}} Yend{ChemEquation}

H. H H ...... H C. H → H.C...H= H C H (2.3) . H H H A Lewis structure of ammonia is also drawn by using the YLewistetrahedralA command. The ﬁrst structure is drawn by using the array environment of the native LATEX2ε,whereYchemradicalA commands are used to draw component radical structures. When inner math modes may cause troubles, the use of the Ymbox command is sometimes useful as follows: Ybegin{ChemEquation} Yraisebox{8pt}{% $Ybegin{array}{ccc} & YchemradicalA[3]{H} & YY[5pt] YchemradicalA[2]{H} & YchemradicalA[124]{Yunderpair{N}} & YchemradicalA[4]{H} YY Yend{array}$} Yquad Yrightarrow Yquad Ymbox{YLewistetrahedralA{0==Yunderpair{N};1==H;2==H;4==H}} Yquad = Yquad Yraisebox{-28pt}{Ytetrahedral{0==Yunderpair{N};1==H;2==H;4==H}} Yend{ChemEquation}

H. H . H...... → . . H N.. H H.N...H= H N.. H (2.4)

The command YLewistetrahedralB is capable of drawing at most four atoms through lone pairs in an alternative mode, where the positions of selected atoms with lone pairs are speciﬁed by its optional argument. The numbering of the four atoms with lone pairs is shown as follows: 14 FUJITA Shinsaku: XΥMTEX

4.. ..1 ..C.. 3 2

The following examples show the applicability of the command YLewistetrahedralB.

YLewistetrahedralB{0==C;1==A;2==B;3==X;4==Y} YqquadYqquad YLewistetrahedralB{0==C;1==A;2==B;3==X} YqquadYqquad YLewistetrahedralB{0==C;1==A;2==B;4==X} YqquadYqquad YLewistetrahedralB{0==C;1==A;3==Y;4==X} YqquadYqquad YLewistetrahedralB{0==C;2==B;3==Y;4==X} YY[15pt] YLewistetrahedralB{0==C;1==A;2==B} YqquadYqquad YLewistetrahedralB{0==C;1==A;3==X} YqquadYqquad YLewistetrahedralB{0==C;1==A;4==X} YqquadYqquad YLewistetrahedralB{0==C;2==B;3==X} YqquadYqquad YLewistetrahedralB{0==C;2==B;4==X} YqquadYqquad YLewistetrahedralB{0==C;3==Y;4==X} YY[15pt] YLewistetrahedralB{0==C;1==A} YqquadYqquad YLewistetrahedralB{0==C;2==B} YqquadYqquad YLewistetrahedralB{0==C;3==B} YqquadYqquad YLewistetrahedralB{0==C;4==B}

Y.. ..A ..AX.. ..AX.. ..AX.. ..C.. ..C.. C.. ..C ..C.. X B X B B Y Y B

..A ..AX.. ..A X.. X.. C.. ..C C ..C.. C.. ..C B X X B B Y

..A B.. C C.. ..C C BB In some cases, YLewistetrahedralB is incapable of accepting a substituent derived from such a command as YlonepairB. To avoid troubles of this type, a rather dirty technique using Ysetbox may be eﬀective, as shown in the following example.

Ybegingroup Yfboxrule=0ptYfboxsep=1pt Ysetbox0=Yhbox{YlonepairB[234]{Yfbox{Ykern0.6pt F}}} Ysetbox1=Yhbox{YlonepairB[134]{Yfbox{Ykern0.6pt F}}} Ysetbox2=Yhbox{YlonepairA[123]{Ykern0.6pt FYkern0.6pt}} Ysetbox3=Yhbox{YLewistetrahedralA{0==B;2==Ybox2}} YLewistetrahedralB{0==Ybox3;3==Yraise1ptYbox0Ykern-1pt;4==Ylower2ptYbox1Ykern-1pt} Yendgroup ...... F...... B.F... ..F.. The following examples show the diﬀerence between YLewistetrahedralA and YlonepairA as well as the diﬀerence between YLewistetrahedralB and YlonepairB.

YLewistetrahedralA{0==C;1=={};2=={};3=={};4=={}}Yquad YLewistetrahedralA{0==C;1=={};2=={};3=={};4=={}}Yquad YlonepairA[1234]{C}YY[10pt] YLewistetrahedralB{0==C;1=={};2=={};3=={};4=={}}Yquad YLewistetrahedralB{0==C;1=={};2=={};3=={};4=={}}Yquad YlonepairB[1234]{C} CHAPTER 2. LONE PAIRS AND RADICALS 15

...... C .C... .C...... C ..C.. ..C..

2.3.3 Nested Tetrahedral Lewis Structures Because the command YLewistetrahedralA is incapable of drawing nested structures, another approach should be taken to to avoid such drawback. For this purpose, the lewisstruc package of the XΥMTEXsystem supports the command YLewisTetrahedralA, which has been deﬁned in an alternative methodology based on the Ytetrahedral command of the aliphat package of the XΥMTEX system. This means that the argument of YLewisTetrahedralA is capable of accommodating a so-called (yl)-function which is widely adopted in the XΥMTEX system. In addition, the argument of YLewisTetrahedralA supports an additional function, which gives us a tool of drawing two pairs of electrons for representing a double bond (D), three pairs of electrons for representing a triple bond (T), and a straight line for representing a single bond.

YLewisTetrahedralA{0==C;1==A;2==B;3==X;4==Y} YLewisTetrahedralA{0==C;1==A;2N==B;3==X;4N==Y} YLewisTetrahedralA{0==C;1D==A;2D==B;3D==X;4D==Y} YLewisTetrahedralA{0==C;1T==A;2T==B;3T==X;4T==Y}

A A.. A.. A...... B.C . YCB YCB.. .. YCB...... Y ...... X X .. X X

By declaring 2==(yl) in an inner YLewisTetrahedralA, a substituent is produced so as to be attached to the 4-position of an outer YLewisTetrahedralA. Thereby, the two tetrahedral Lewis structures are linked to each other as follows:

YLewisTetrahedralA{0==C;1==A;2==B;3==X;% 4==YLewisTetrahedralA{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralA{0==C;1==A;2==B;3==X;% 4D==YLewisTetrahedralA{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralA{0==C;1==A;2==B;3==X;% 4T==YLewisTetrahedralA{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralA{0==C;1==A;2==B;3==X;% 4N==YLewisTetrahedralA{2==(yl);0==C;1==A;3==X;4==Y}}

A.. A A.. A A.. A A.. A ...... B.C.. . C.. . Y B.C.. .. C.. . Y B.C.. ... C.. . Y B.C.. C.. . Y X X X X X X X X

By declaring 4==(yl) in an inner YLewisTetrahedralA, another substituent is produced so as to be attached to the 2-position of an outer YLewisTetrahedralA. Thereby, the two tetrahedral Lewis structures are linked to each other as follows:

YLewisTetrahedralA{0==C;1==A;4==B;3==X;% 2==YLewisTetrahedralA{4==(yl);0==C;1==A;3==X;2==Y}} YLewisTetrahedralA{0==C;1==A;4==B;3==X;% 2D==YLewisTetrahedralA{4==(yl);0==C;1==A;3==X;2==Y}} 16 FUJITA Shinsaku: XΥMTEX

YLewisTetrahedralA{0==C;1==A;4==B;3==X;% 2T==YLewisTetrahedralA{4==(yl);0==C;1==A;3==X;2==Y}} YLewisTetrahedralA{0==C;1==A;4==B;3==X;% 2N==YLewisTetrahedralA{4==(yl);0==C;1==A;3==X;2==Y}}

A A A A A A A A ...... Y.C.. .C.. . B Y.C.. ..C.. . B Y.C.. ...C.. . B Y.C.. C.. . B X X X X X X X X

Lewis structures of vertical linkage can be drawn in a similar way.

YLewisTetrahedralA{0==C;2==A;4==B;3==X;% 1==YLewisTetrahedralA{3==(yl);0==C;1==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;3==X;% 1D==YLewisTetrahedralA{3==(yl);0==C;1==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;3==X;% 1T==YLewisTetrahedralA{3==(yl);0==C;1==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;3==X;% 1N==YLewisTetrahedralA{3==(yl);0==C;1==A;4==X;2==Y}} A A A.. .. A ...... Y.C . X Y C X Y.C . X Y C.. X ...... A.C.. . B A.C.. . B A.C.. . B A.C.. . B X X X X

Another set of Lewis structures of vertical linkage can be drawn in a similar way.

YLewisTetrahedralA{0==C;2==A;4==B;1==X;% 3==YLewisTetrahedralA{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;1==X;% 3D==YLewisTetrahedralA{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;1==X;% 3T==YLewisTetrahedralA{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralA{0==C;2==A;4==B;1==X;% 3N==YLewisTetrahedralA{1==(yl);0==C;3==A;4==X;2==Y}}

X X X X ...... A.C.. . B A.C.. . B A.C.. . B A.C . B ...... Y.C.. . X Y.C . X . . .. Y.C.. . X . . A A Y C.. X A A Because the command YLewistetrahedralB is incapable of drawing nested structures, another approach should be taken to to avoid such drawback. For this purpose, the lewisstruc package of the XΥMTEX system supports the command YLewisTetrahedralB, which has been deﬁned in an alternative methodology based on the Ysquareplanar command (renamed from Ysquare)ofthealiphat package of the XΥMTEX system. This means that the argument of YLewisTetrahedralB is capable of accommodating a so-called (yl)-function which is widely adopted in the XΥMTEX system. In addition, the argument of YLewisTetrahedralB supports an additional function, which gives us a tool of drawing two pairs of electrons for representing a double bond (D), three pairs of electrons for representing a triple bond (T), and a straight line for representing a single bond. CHAPTER 2. LONE PAIRS AND RADICALS 17

YLewisTetrahedralB{0==C;1==A;2==B;3==X;4==Y} YLewisTetrahedralB{0==C;1==A;2N==B;3==X;4N==Y} YLewisTetrahedralB{0==C;1D==A;2D==B;3D==X;4D==Y} YLewisTetrahedralB{0==C;1T==A;2T==B;3T==X;4T==Y}

Y Y A Y. ..A Y.. ..A ..A ...... C. .C ...C...... C.... X B X X B . . B X B

By declaring 2==(yl) in an inner YLewisTetrahedralB, a substituent is produced so as to be attached to the 4-position of an outer YLewisTetrahedralB. Thereby, the two tetrahedral Lewis structures are linked to each other as follows:

YLewisTetrahedralB{0==C;1==A;2==B;3==X;% 4==YLewisTetrahedralB{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralB{0==C;1==A;2==B;3==X;% 4D==YLewisTetrahedralB{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralB{0==C;1==A;2==B;3==X;% 4T==YLewisTetrahedralB{2==(yl);0==C;1==A;3==X;4==Y}} YLewisTetrahedralB{0==C;1==A;2==B;3==X;% 4N==YLewisTetrahedralB{2==(yl);0==C;1==A;3==X;4==Y}}

Y. .A Y.. ..A Y. .A Y.. ..A . . .C . . .C. ..C...... C.. ..A ...... A X ... ..A X ..A X ..C.. X ..C.. ..C.. ..C.. X B X B X B X B

By declaring 4==(yl) in an inner YLewisTetrahedralB, another substituent is produced so as to be attached to the 2-position of an outer YLewisTetrahedralB. Thereby, the two tetrahedral Lewis structures are linked to each other as follows:

YLewisTetrahedralB{0==C;1==A;4==B;3==X;% 2==YLewisTetrahedralB{4==(yl);0==C;1==A;3==X;2==Y}} YLewisTetrahedralB{0==C;1==A;4==B;3==X;% 2D==YLewisTetrahedralB{4==(yl);0==C;1==A;3==X;2==Y}} YLewisTetrahedralB{0==C;1==A;4==B;3==X;% 2T==YLewisTetrahedralB{4==(yl);0==C;1==A;3==X;2==Y}} YLewisTetrahedralB{0==C;1==A;4==B;3==X;% 2N==YLewisTetrahedralB{4==(yl);0==C;1==A;3==X;2==Y}}

B.. ..A B.. ..A B.. ..A B.. ..A ..C.. ..A ..C... .A ..C... ..C .C ...... A .A X . . X ..C.. X .C . X . X Y X Y . . ..C.. X Y X Y

Lewis structures of northeast linkage can be drawn in a similar way.

YLewisTetrahedralB{0==C;2==A;4==B;3==X;% 1==YLewisTetrahedralB{3==(yl);0==C;1==A;4==X;2==Y}} YLewisTetrahedralB{0==C;2==A;4==B;3==X;% 1D==YLewisTetrahedralB{3==(yl);0==C;1==A;4==X;2==Y}} 18 FUJITA Shinsaku: XΥMTEX

YLewisTetrahedralB{0==C;2==A;4==B;3==X;% 1T==YLewisTetrahedralB{3==(yl);0==C;1==A;4==X;2==Y}} YLewisTetrahedralB{0==C;2==A;4==B;3==X;% 1N==YLewisTetrahedralB{3==(yl);0==C;1==A;4==X;2==Y}}

X A X A X. .A .. .. X.. ..A ...... C.. B B .C . B ...C.. B .. ..C...... Y .. Y ..C.. Y ..C.. Y ..C.. ..C.. X A X A X A X A

Another set of Lewis structures of southwest linkage can be drawn in a similar way.

YLewisTetrahedralB{0==C;2==A;4==B;1==X;% 3==YLewisTetrahedralB{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralB{0==C;2==A;4==B;1==X;% 3D==YLewisTetrahedralB{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralB{0==C;2==A;4==B;1==X;% 3T==YLewisTetrahedralB{1==(yl);0==C;3==A;4==X;2==Y}} YLewisTetrahedralB{0==C;2==A;4==B;1==X;% 3N==YLewisTetrahedralB{1==(yl);0==C;3==A;4==X;2==Y}}

B.. ..X B.. ..X B.. ..X B.. ..X X.. ..C.. X. ...C.. ...C.. C.. .C . . . X.. ... X. . . A ..C.. A .C . A . A A Y A Y . . ..C.. A Y A Y

A rather dirty technique is necessary to draw a Lewis structure of boron triﬂuoride.

Ybegingroup Yfboxrule=0ptYfboxsep=1pt YLewisTetrahedralB{% 0==BYLewisSbondYraisebox{-1.3pt}{YlonepairA[123]{Yfbox{Ykern0.6pt F}}};% 3==Yraisebox{1.6pt}{YlonepairB[234]{Yfbox{Ykern0.6pt F}}}Ykern-2pt;% 4==Yraisebox{-1.9pt}{YlonepairB[134]{Yfbox{Ykern0.6pt F}}}Ykern-2pt} %% YLewisTetrahedralB{% 0==BYsbondYraisebox{-1.3pt}{YlonepairA[123]{Yfbox{Ykern0.6pt F}}};% 3N==Yraisebox{1.6pt}{YlonepairB[234]{Yfbox{Ykern0.6pt F}}}Ykern-2pt;% 4N==Yraisebox{-1.9pt}{YlonepairB[134]{Yfbox{Ykern0.6pt F}}}Ykern-2pt} Yendgroup

...... F ..F...... B. F... B F... ..F...... F..

2.4 Additional Examples for Compounds with Lone Pairs

1-Isothiocyanato-(4S)-(methylsulfonyl)butane (an anti-cancer agent contained in broccoli) has the following structure: CHAPTER 2. LONE PAIRS AND RADICALS 19

Ybegin{XyMcompd}(1300,450)(100,100){}{} YdtetrahedralS{0==S;1D==YlonepairA[24]{O};4B==CH$_{3}$;3A==YlonepairB[1]{Ynull};% 2==Ytetramethylene{}{1==(yl);4W==YlonepairA[3]{N}Ydbond CYdbondYlonepairA[13]{S}}} Yend{XyMcompd} Yqquad Ybegin{XyMcompd}(1400,450)(100,100){}{} YdtetrahedralS{0==S;1D==YlonepairA[24]{O};4B==CH$_{3}$;3A==YlonepairB[1]{Ynull};% 0==Yphantom{S}% Yraisebox{-0.4em}{% Ypentamethylenei{}{1==(yl);5W==YlonepairA[3]{N}Ydbond CYdbondYlonepairA[13]{S}}}} Yend{XyMcompd}

.O. .O. S .. S .. N C S ...... N.. C ..S CH3 CH3 The latter structure has a more plausible length of an S—C bond. An alternative code can typeset the same compound:

Ybegin{XyMcompd}(1400,450)(100,100){}{} YdtetrahedralS{0==% Ypentamethylenei{1==S}{1==(yl);5W==YlonepairA[3]{N}Ydbond CYdbondYlonepairA[13]{S}};% 1D==YlonepairA[24]{O};4B==CH$_{3}$;3A==YlonepairB[1]{Ynull}} Yend{XyMcompd}

.O.

. S .. . N.. C ..S CH3 The S O bond of a sulfoxide can be regarded as being delocalized to give S+ O−. For example, the sulfoxide part of sparsomycin is drawn by means of the following code:

Ybegin{XyMcompd}(2100,800)(100,200){}{} Ysixheterov[a]{4==Ydownnobond{N}{H};6==Yllap{H}{N}; 2s==Ynonamethylene[b]{5==Ydownnobond{N}{H};8==Ydownnobond{S}{$^{+}$};% 9s==Ytrimethylene{2==S}{1==(yl)}} {1==(yl);4D==O;6SA==H;6==Ydimethylenei{1==Yupnobond{O}{H}}{2==(yl)};% 8SB==Yllap{$^{-Y:}$}YlonepairA[124]{O};8SA==Ykern4ptYnelonepair}}% {1==CH$_{3}$;3D==O;5D==O} Yend{XyMcompd} H O −.... CH3 O H .O. .. S S HN N + H

O N O H It should be noted that the organochemical convention allows us to omit lone pairs if unnecessary. Thus, the nitrogen atoms and the oxygen atoms (except the oxygen of the sulfoxide moiety) in the above structural formula of sparsomycin have no information on lone pairs. As a further example, the formula of 1-isothiocyanato-(4S)-(methylsulfonyl)butane is allowed to be represented by an abbreviated form, where the lone pairs except that of the sulfur atom (necessary to show the (4S)-conﬁguration) are omitted as follows. 20 FUJITA Shinsaku: XΥMTEX

Ybegin{XyMcompd}(1400,450)(100,100){}{} YdtetrahedralS{0==% Ypentamethylenei{1==S}{1==(yl);5W==NYdbond CYdbond S};% 1D==O;4B==CH$_{3}$;3A==YlonepairB[1]{Ynull}} Yend{XyMcompd} Yreactlrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(1400,450)(100,100){}{} YdtetrahedralS{0==% Ypentamethylenei{1==SYrlap{$^{+}$}}{1==(yl);5W==NYdbond CYdbond S};% 1==O$^{-}$;4B==CH$_{3}$;3A==YlonepairB[1]{Ynull}} Yend{XyMcompd}

O O−

S S+ .. N C S .. N C S CH3 CH3 The right canonical formula shows that unnecessary lone pairs can be omitted even for canonical formulas with formal charges (cf. Section 3.1 on page 21). Chapter 3

Chemical Schemes with Lewis Structures

3.1 Resonance Forms

For an approximation of quantum-chemical calculation, organic chemistry uses a resonance form in which two or more representative structural formulas (canonical formulas) are linked with double-headed arrows. For example, nitromethane is represented by the following resonance form, where two structural formulas with formal charges are linked by a double-headed arrow so as to show the neutral nature of the nitromethane molecule.

Ybegin{XyMcompd}(450,450)(0,100){}{} YRtrigonal{0==N$^{Y:+}$;1==H$_{3}$C;3D==O;2==O$^{-}$} Yend{XyMcompd} Yreactlrarrow{0pt}{3cm}{arrow for}{a resonance form} Ybegin{XyMcompd}(450,450)(0,100){}{}Yquad YRtrigonal{0==N$^{Y:+}$;1==H$_{3}$C;2D==O;3==O$^{-}$} Yend{XyMcompd}

O O−

+ arrow for + H3C N H3C N a resonance form O− O The above resonance form is an abbreviated representation of the following resonance form with full information of lone pairs, where two Lewis structures are linked with a double-headed arrow.

Ybegin{XyMcompd}(450,450)(0,100){}{} YRtrigonal{0==N$^{Y:+}$;1==H$_{3}$C;3D==YlonepairA[12]{O};2==YlonepairA[234]{O}$_{Y:-}$} Yend{XyMcompd} Yreactlrarrow{0pt}{3cm}{arrow for}{a resonance form} Ybegin{XyMcompd}(450,450)(0,100){}{}Yquad YRtrigonal{0==N$^{Y:+}$;1==H$_{3}$C;2D==YlonepairA[23]{O};3==YlonepairA[124]{O}$^{Y:-}$} Yend{XyMcompd} .. .. O. .O.−

+ arrow for + H3C N H3C N a resonance form . . . .O...− O... 21 22 FUJITA Shinsaku: XΥMTEX

Note that lone pairs around each central nitrogen are replaced by usual bonds ( and )anda polarized bond (N+ O−). A bent arrow (curved arrow) is used to explain the relationship between the two Lewis structures, where the start of the arrow is located at a lone pair to be shifted and the arrowhead is located at a bond to be formed in one case; or, in the other case, the start of the arrow is located at a bond to be deleted and the arrowhead is located at a lone pair to be formed. The following example is to show such an explanation.

Ybegin{center} Ybegin{XyMcompd}(450,450)(0,100){}{} YRtrigonal{0==N$^{Y:+}$;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (90,150)(70,250)(150,250);% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (110,-70)(50,-130)(140,-160);% 1==H$_{3}$C;3D==YlonepairA[12]{O};2==YlonepairA[234]{O}$_{Y:-}$} Yend{XyMcompd} Yreactlrarrow{0pt}{3cm}{arrow for}{a resonance form} Ybegin{XyMcompd}(450,450)(0,100){}{}Yquad YRtrigonal{0==N$^{Y:+}$;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (120,140)(70,240)(130,250);% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (100,-70)(50,-130)(140,-170);% 1==H$_{3}$C;2D==YlonepairA[23]{O};3==YlonepairA[124]{O}$^{Y:-}$} Yend{XyMcompd} Yend{center} where each red bent arrow is drawn by the Ypscurve command supported by the PSTricks package [12], which is loaded automatically when Yusepackage{xymtexps} is declared to load the XΥMTEXsystemof POSTSCRIPT-compatible mode. The resulting output is shown as follows: .. .. O. .O.−

+ arrow for + H3C N H3C N a resonance form . . . .O...− O... Another resonance form can be drawn as follows, where a three-membered canonical formula is in- volved. Note that the three atoms of the resulting three-membered ring (the right-hand formula) are located at the same positions of the left-handed open-chain formula.

Ybegin{center} Ybegin{XyMcompd}(450,450)(0,100){}{} YRtrigonal{0==N$^{Y:+}$;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{<-}% (30,80)(30,160)(90,150);% 2==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{->}% (100,30)(150,100)(150,170)(80,250);% 1==H$_{3}$C;3D==YlonepairA[12]{O};2==YlonepairA[234]{O}$_{Y:-}$} Yend{XyMcompd} Yqquad Yreactlrarrow{0pt}{3cm}{arrow for}{a resonance form} Ybegin{XyMcompd}(450,450)(0,100){}{}Yquad YRtrigonal{0==YlonepairA[1]{N};% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{->}% (30,100)(20,160)(100,150);% 2==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{<-}% CHAPTER 3. CHEMICAL SCHEMES WITH LEWIS STRUCTURES 23

(100,30)(150,100)(150,170)(70,250);% 1==H$_{3}$C;2==YlonepairA[23]{O};3==YlonepairA[12]{O};% 2==Ypsline[unit=Yunitlength,linewidth=0.4pt](40,90)(40,380)} Yend{XyMcompd} Yend{center} where in the vertical bond in the right-hand formula is drawn by using Ypsline supported by the PSTricsks package. .. .. O. O.

+ arrow for .. H3C N H3C N a resonance form . . . .O...− O... In standard viewpoints of organic chemistry, such a three-membered canonical formula is recognized not to exhibit so large contribution to a resonance form. If such a three-membered ring has N—O and O—O bonds of ordinary bond lengths for three-membered rings, the same electron shift as above should be regarded as an equilibrium so that the two Lewis structures are not canonical formulas for constructing a resonance form: Ybegin{center} Ybegin{XyMcompd}(450,450)(0,100){}{} YRtrigonal{0==N$^{Y:+}$;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{<-}% (30,80)(30,160)(90,150);% 2==Ypscurve[unit=Yunitlength,linewidth=0.4pt]{->}% (100,30)(150,100)(150,170)(80,250);% 1==H$_{3}$C;3D==YlonepairA[12]{O};2==YlonepairA[234]{O}$_{Y:-}$} Yend{XyMcompd} Yqquad Yreactlarrow{0pt}{3cm}{% Yreactrarrow{0pt}{1.5cm}{}{}YY[-8pt]}{Ystrut}Yqquad Ybegin{XyMcompd}(450,300)(50,200){}{} Ythreeheterohi{1==YlonepairA[1]{N};2==YlonepairA[23]{O};3==YlonepairA[12]{O}}% {1==H$_{3}$C} Yend{XyMcompd} Yend{center} .. . O ... arrow for .. O. + H3C N H3C N an equilibrium O...... O...− p-Methoxybenzaldehyde exhibits delocalization through the benzene ring, where the electron-donating methoxy interacts the electron-withdrawing carbonyl group according to the following resonance form: Ybegin{XyMcompd}(1100,350)(-100,250){}{} Ybzdrh{1==CH$_{3}$YlonepairA[13]{O};% 4==Yrtrigonal{1==(yl);0==C;2==H;3D==YlonepairA[13]{O}}} Yend{XyMcompd} Yreactlrarrow{0pt}{1cm}{}{} Yquad Ybegin{XyMcompd}(1150,350)(-150,250){}{} Ybzdrh[pa]{1D==CH$_{3}$YlonepairA[3]{O}$^{+}$;% 4D==Yrtrigonal{1==(yl);0==C;2==H;3==YlonepairA[123]{O}Yrlap{$^{Y:-}$}}} Yend{XyMcompd} Yreactlrarrow{0pt}{1cm}{}{} Yquad etc...... − O.. O... .. + CH3O.. C CH3O.. C etc. H H 24 FUJITA Shinsaku: XΥMTEX 3.2 Radical Fissions

A radical ﬁssion of a C—H bond of methane is represented in two ways, i.e., a scheme due to Lewis structures and a scheme due to usual structural formulas.

Ybegin{ChemEquation} Ybegin{XyMcompd}(250,400)(150,100){}{} YdtetrahedralS{0==C;1==H;2==H;3A==H;4B==H} Yend{XyMcompd} Yqquad = Yqquad YleftY{% Ybegin{array}{ccc} Ybegin{XyMcompd}(100,200)(100,-50){}{} Yput(0,0){Yblue Ycircle{30}} Yput(0,0){YLewistetrahedralA{0==C;1==H;2==H;3==H;4==H}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (185,70)(200,150)(240,80) Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (170,0)(200,-80)(220,-50)(190,0) Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{energy}{$YDelta Ymathit{H}^{Ycirc}=439~kJ/mol$} & Ysetbox0=Yhbox{YchemradicalA[2]{C}} Ybegin{XyMcompd}(100,200)(100,-50){}{} YLewistetrahedralA{0==Ybox0;1==H;3==H;4==H} Yend{XyMcompd} + Yquad YchemradicalA[4]{H} YY Ynoalign{Yvskip8pt} Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==C;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (40,70)(80,150)(120,50);% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (140,50)(170,150)(220,70);% 1==H;2==H;3==H;4==H} Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{energy}{$YDelta Ymathit{H}^{Ycirc}=439~kJ/mol$} & Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==YchemradicalA[2]{C};1==H;2==H;3==H} Yend{XyMcompd} + Yquad YchemradicalA[4]{H} YY Yend{array}Yright. Yend{ChemEquation}

Because the XyMcompd environment is based on the picture environment of LATEX2ε, commands of LATEX2ε such as Yput and Ycircle can be used in addition to commands of XΥMTEX. Thus, the command Yput(0,0){Yblue Ycircle{30}} outputs a blue circle at the original point. Moreover, commands of PSTricks package (e.g., Ypscurve) can be declared directly in the XyMcompd environment. CHAPTER 3. CHEMICAL SCHEMES WITH LEWIS STRUCTURES 25

⎧ H.. energy H.. ⎪ b . . . . . ⎪ H.C...H ◦ H.C.. + H H ⎪ ΔH = 439 kJ/mol ⎨⎪ H H C = H H (3.1) H H ⎪ energy ⎪ . . H ⎪ H C H ◦ H C + H ⎩⎪ ΔH = 439 kJ/mol H H

It should be noted that each bent arrow in a radical ﬁssion represents the shift of a single electron, while each bent arrow in a resonance form represents the shift of a lone pair (two electrons). Bent arrows of the former type are usually represented as harpoons (e.g., ), which are not supported by the PSTricks package. This will be an open target to be developed.

3.3 Carbocations

A carbocation can be dissociated from methane by extracting a hydride ion. Two expressions of such dissociation are shown as follows:

Ybegin{ChemEquation} YleftY{% Ybegin{array}{ccc} Ybegin{XyMcompd}(100,200)(100,-50){}{} Yput(0,0){YLewistetrahedralA{0==C;1==H;2==H;3==H;4==H}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (185,70)(200,150)(240,80) Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{}{} & Ybegin{XyMcompd}(100,200)(100,-50){}{} YLewistetrahedralA{0==CYrlap{$^{+}$};1==H;3==H;4==H} Yend{XyMcompd} + Yquad YlonepairA[4]{H}^{-} YY Ynoalign{Yvskip8pt} Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==C;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (140,50)(170,150)(220,70);% 1==H;2==H;3==H;4==H} Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{}{} & Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==CYrlap{$^{+}$};1==H;2==H;3==H} Yend{XyMcompd} + Yquad YlonepairA[4]{H}^{-} YY Yend{array}Yright. Yend{ChemEquation} 26 FUJITA Shinsaku: XΥMTEX

⎧ H H.. ⎪ .... . + . − ⎪ H.C...H H.C.. + .H ⎪ ⎨⎪ H H H H (3.2) ⎪ ⎪ + . − ⎪ H C H H C + H ⎩⎪ H H The addition of hydrogen chloride to 2,3-dimethylbut-2-ene produces 2-chloro-2,3-dimethylbutane, where the ﬁrst protonation produces a carbocation, which is converted to the ﬁnal product by chlorination.

Ybegin{center} Ybegin{XyMcompd}(800,700)(50,100){}{} Yput(600,700){HYsbondYlonepairA[123]{Cl}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=green]{->}% (400,330)(400,600)(600,730)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=green]{->}% (750,720)(800,600)(850,700)% Yput(0,0){YEthyleneh{}{1==CH$_{3}$;2==CH$_{3}$;3==CH$_{3}$;4==CH$_{3}$}} Yend{XyMcompd} Yreactlarrow{-15pt}{3cm}{% Yreactrarrow{0pt}{1.5cm}{}{}YY[-8pt]}{protonation}Yqquad Ybegin{XyMcompd}(850,700)(50,100){}{} Yput(750,700){YlonepairA[1234]{Cl}$^{Y:-}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (500,330)(500,600)(700,730)% Yput(0,0){% YLtrigonal{0==C$^{+}$;1==Ytetrahedral{2==(yl);0==C;1==H;4==CH$_{3}$;3==CH$_{3}$};% 2==CH$_{3}$;3==CH$_{3}$}} Yend{XyMcompd} YY Yreactrarrow{0pt}{3cm}{Ystrut}{{}YY[-18pt]% Yreactlarrow{0pt}{1.5cm}{}{chlorination}}Yqquad Ybegin{XyMcompd}(900,500)(-50,100){}{} Ytetrahedral{0==C;4==Ytetrahedral{2==(yl);0==C;1==H;4==CH$_{3}$;3==CH$_{3}$};% 1==YlonepairA[124]{Cl};2==CH$_{3}$;3==CH$_{3}$} Yend{XyMcompd} Yend{center}

...... − H Cl.. . .Cl.. .

CH3 CH3 CH3 H

+ CC C C CH3 protonation CH3 CH3 CH3 CH3 .. .Cl. H

CH3 C C CH3 chlorination CH3 CH3 3.4 Nucleophilic Substitutions of Order Two

An acid-catalyzed bromination (bromine substitution) of ethanol runs through an SN2 mechanism, which causes the stereochemical inversion of the central carbon, although the case of ethanol exhibits no eﬀect of such an inversion. CHAPTER 3. CHEMICAL SCHEMES WITH LEWIS STRUCTURES 27

Ybegin{XyMcompd}(900,450)(100,100){}{} Yput(0,0){YltetrahedralS{0==C;2==H$_{3}$C;3A==H;4B==H;1==YlonepairA[13]{O}H}} Yput(650,275){+} Yput(750,275){HYsbond YlonepairA[123]{Br}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (500,370)(575,450)(675,450)(750,370)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (900,350)(950,450)(1000,380)% Yend{XyMcompd} Yqquad Yreactrarrow{0pt}{3cm}{Ystrut}{{}YY[-18pt]% Yreactlarrow{0pt}{1.5cm}{}{}}Yqquad Ybegin{XyMcompd}(900,450)(100,100){}{} Yput(0,0){YltetrahedralS{0==C;2==H$_{3}$C;3A==H;4B==H;% 1==Yllap{Yraisebox{2pt}{$^{Y:+}$}}YlonepairA[3]{O}H$_{2}$}} Yput(780,275){+} Yput(950,275){YlonepairA[1234]{Br}$^{Y:-}$} Yend{XyMcompd} YY Ybegin{XyMcompd}(900,450)(100,100){}{} Yput(400,0){YltetrahedralS{0==C;2==H$_{3}$C;3A==H;4B==H;% 1==Yllap{Yraisebox{2pt}{$^{Y:+}$}}YlonepairA[3]{O}H$_{2}$}} %Yput(800,275){+} Yput(100,200){YlonepairA[1234]{Br}$^{Y:-}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (200,300)(350,400)(500,400)(650,320)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (775,310)(820,450)(900,350)% Yend{XyMcompd} Yqquad Yreactrarrow{0pt}{3cm}{S$_{Ymathrm{N}}$2}{{}YY[-18pt]% Yreactlarrow{0pt}{1.5cm}{}{}}Yqquad Ybegin{XyMcompd}(900,450)(100,100){}{} Yput(0,0){YrtetrahedralS{0==C;2==CH$_{3}$;3A==H;4B==H;% 1==YlonepairA[134]{Br}}} Yput(700,275){+} Yput(870,275){H$_{2}$YlonepairA[13]{O}} Yend{XyMcompd}

H3C H3C .. .. . + . .. .− C O..H +H Br.. . C O..H2 + .Br.. . H H H H H3C CH3 SN2 + ...... − C O..H2 .Br.. C +H2O.. .Br.. . H H H H 3.5 Carboanions

A carboanion can be dissociated from methane by extracting a proton. Two expressions of such dissociation are shown as follows:

Ybegin{ChemEquation} YleftY{% 28 FUJITA Shinsaku: XΥMTEX

Ybegin{array}{ccc} Ybegin{XyMcompd}(100,200)(100,-50){}{} Yput(0,0){YLewistetrahedralA{0==C;1==H;2==H;3==H;4==H}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (170,0)(200,-80)(220,-50)(190,0) Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{}{} & Ysetbox0=Yhbox{YlonepairA[2]{C}Yrlap{$^{Y:-}$}} Ybegin{XyMcompd}(100,200)(100,-50){}{} YLewistetrahedralA{0==Ybox0;1==H;3==H;4==H} Yend{XyMcompd} + H^{+} YY Ynoalign{Yvskip8pt} Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==C;% 0==Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (40,70)(80,150)(120,50);% 1==H;2==H;3==H;4==H} Yend{XyMcompd} & Yreactrarrow{0pt}{4cm}{}{} & Ybegin{XyMcompd}(350,450)(100,100){}{} Ytetrahedral{0==YlonepairA[2]{C}$^{Y:-}$;1==H;2==H;3==H} Yend{XyMcompd} + Yquad H^{+} YY Yend{array}Yright. Yend{ChemEquation}

⎧ H H.. ⎪ ...... − + ⎪ H.C...H H.C... +H ⎪ ⎨⎪ H H H H (3.3) ⎪ ⎪ .− + ⎪ H C H H C. +H ⎩⎪ H H 3.6 Aromatic Nucleophilic Substitutions

Aromatic nucleophilic substitutions have been already discussed in Chapter 4 of the online manual of XΥMTEX version 4.01 (xymtx401.pdf). The present section provides further examples in which lone pairs are drawn explicitly. A methoxide anion attacks 1-chloro-2,4-dinitrobenzene at the carbon atom attached by chlorine so as to give a Meisenheimer complex, in which the resulting negative charge is delocalized through the benzene ring by the nitro groups.

Ybegin{ChemEqnarray} Ylefteqn{% Ybegin{XyMcompd}(850,900)(-50,0){}{} Yput(0,0){Ybzdrv{4==YlonepairA[234]{Cl};3==NO$_{2}$;1==NO$_{2}$}} Yput(-100,0){CH$_{3}$YlonepairA[123]{O}$^{Y:-}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (120,100)(180,200)(380,230)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% CHAPTER 3. CHEMICAL SCHEMES WITH LEWIS STRUCTURES 29

(240,350)(300,450)(335,335)% Yend{XyMcompd} Yreactrarrow{0pt}{2cm}{Ystrut}{CH$_{3}$OH}}&& Ynonumber YY && Yleft[% Ybegin{XyMcompd}(650,900)(150,0){}{} Yput(0,0){Ybzdrv[od]{4Sb==CH$_{3}$YlonepairA[23]{O};% 4Sa==YlonepairA[234]{Cl};3==NO$_{2}$;1==NO$_{2}$}} Yput(150,320){$_{Y:-}$YlonepairB[1]{~}} Yend{XyMcompd} Yreactlrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(650,900)(150,0){}{} Yput(0,0){Ybzdrv[pa]{4Sb==CH$_{3}$YlonepairA[23]{O};% 4Sa==YlonepairA[234]{Cl};3==NO$_{2}$;1==NO$_{2}$}} Yput(305,620){$^{Y:-}$YlonepairA[3]{~}} Yend{XyMcompd} Yreactlrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(650,900)(150,0){}{} Yput(0,0){Ybzdrv[oc]{4Sb==CH$_{3}$YlonepairA[23]{O};% 4Sa==YlonepairA[234]{Cl};3==NO$_{2}$;1==NO$_{2}$}} Yput(538,320){YlonepairB[4]{~}$^{Y:-}$} Yend{XyMcompd}YquadYright] = Ybegin{XyMcompd}(650,900)(150,0){}{} Yput(0,0){Ybzdrv[Z]{4Sb==CH$_{3}$YlonepairA[23]{O};% 4Sa==YlonepairA[234]{Cl};3==NO$_{2}$;1==NO$_{2}$}} Yput(400,450){Ymakebox(0,0){Yscriptsize $-$}} Ypsline[unit=Yunitlength,linewidth=0.4pt,linestyle=dashed,dash=2pt 1pt]{-}% (250,350)(250,530)(400,620)(550,530)(550,350)% Yend{XyMcompd} Yend{ChemEqnarray}

NO2

CH3OH NO2 .. .− . . CH3O... Cl.. ⎡ ⎤ NO2 NO2 NO2 NO2 ⎢ ⎥ ⎢ − ⎥ ⎢ .. ⎥ ⎢ ⎥ ⎢ ⎥ ⎢ ⎥ = − (3.4) ⎢ . . − ⎥ ⎢ − . . ⎥ ⎢ ⎥ ⎣ NO2 NO2 NO2 ⎦ NO2 ...... CH3O... .Cl.. . CH3O... .Cl.. . CH3O... .Cl.. . CH3O... .Cl.. .

The Chichibabin reaction is a 2-amination of pyridine by means of potassium amide to produce 2-aminopyridine.

Ybegin{center} Ybegin{XyMcompd}(950,500)(150,150){}{} Yput(0,0){Ysixheterovi[ace]{1==YlonepairA[3]{N}}{}} Yput(700,300){$^{Y:-}$YlonepairA[13]{N}H$_{2}$} 30 FUJITA Shinsaku: XΥMTEX

Yput(1050,300){K$^{+}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (590,350)(700,450)(810,390)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (410,300)(450,450)(480,380)% Yend{XyMcompd} Yreactrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(950,500)(150,150){}{} Yput(0,0){Ysixheterovi[ce]{1==Yllap{$_{-}$}YlonepairA[13]{N}}{% 2Sa==YlonepairA[1]{N}H$_{2}$;2Sb==H}} Yput(950,100){K$^{+}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (410,200)(450,120)(510,290)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (610,260)(650,100)(790,100)(850,120)% Yend{XyMcompd} Yreactrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(1000,500)(150,150){}{} Yput(0,0){Ysixheterovi[ace]{1==YlonepairA[3]{N}}{% 2==YlonepairA[1]{N}H$_{2}$}} Yput(950,100){K$^{+}$~$^{-Y:}$YlonepairA[4]{H}} Yend{XyMcompd} YY Yvskip15pt Yreactrarrow{0pt}{1cm}{}{} Ybegin{XyMcompd}(1050,500)(150,150){}{} Yput(0,0){Ysixheterovi[ace]{1==YlonepairA[3]{N}}{% 2==Yllap{$_{-}$}YlonepairA[13]{N}H}} Yput(900,100){K$^{+}$ + H$_{2}$} Yend{XyMcompd} Yreactrarrow{0pt}{1cm}{H$_{2}$YlonepairA[12]{O}}{Ystrut} Ybegin{XyMcompd}(700,500)(150,150){}{} Yput(0,0){Ysixheterovi[ace]{1==YlonepairA[3]{N}}{% 2==YlonepairA[1]{N}H$_{2}$}} Yend{XyMcompd} +HYlonepairA[123]{O}$^{Y:-}$ Yend{center}

− .. + .. N..H2 K .. NH2 .. N −N N .. .. H .. NH2 K+ K+ −.H

... H2O. .. +HO.− ...... N.. −N..H N.. NH2 + K +H2 3.7 Further Reactions 3.7.1 Formation and Reactions of Diazoketones The reaction of diazomethane with an acid chloride results in subsequent processes of addition, elimination, and deprotonation so as to give a diazoketone as follows:

Ybegin{quote} CHAPTER 3. CHEMICAL SCHEMES WITH LEWIS STRUCTURES 31

Ybegin{XyMcompd}(700,600)(100,0){}{} Yput(0,0){YDtrigonal{0==C;1D==YlonepairB[14]{O};3==R;2==YlonepairA[123]{Cl}}} Yput(171,-50){$^{-}$YlonepairA[1]{C}H$_{2}$Ysbond N$^{+}$YtbondYlonepairA[2]{N}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (220,50)(180,150)(300,250)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (350,400)(400,450)(350,500)% Yend{XyMcompd} Yreactrarrow{0pt}{2cm}{addition}{Ystrut} Ybegin{XyMcompd}(800,500)(100,50){}{} Yput(0,0){Ytetrahedral{0==C;1==YlonepairA[124]{O}$^{Y:-}$;2==R;4==YlonepairA[123]{Cl};% 3==CH$_{2}$Ysbond N$^{+}$YtbondYlonepairA[2]{N}}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (400,310)(450,400)(550,360)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (300,400)(400,450)(350,500)% Yend{XyMcompd} Yreactrarrow{0pt}{2cm}{elimination}{Ystrut} Ybegin{XyMcompd}(800,600)(100,-50){}{} Yput(0,0){YDtrigonal{0==C;1D==YlonepairB[14]{O};3==R;% 2==Ysquareplanar{4==(yl);0==C;1==H;3==H;2==N$^{+}$YtbondYlonepairA[2]{N}}}} Yput(600,450){YlonepairA[1234]{Cl}$^{Y:-}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (500,180)(540,300)(600,250)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (680,360)(750,400)(700,450)% Yend{XyMcompd} YY Yvskip10pt Yreactrarrow{0pt}{2cm}{deprotonation}{Ystrut} Ybegin{XyMcompd}(900,400)(100,150){}{} Yput(0,0){YDtrigonal{0==C;1D==YlonepairB[14]{O};3==R;% 2==Yllap{$_{-}$}YlonepairA[3]{C}HYsbond N$^{+}$YtbondYlonepairA[2]{N}}} Yend{XyMcompd} +HYsbondYlonepairA[123]{Cl} Yend{quote} ...... − . .− O .O. O .Cl.. . addition .. . elimination C H C R C Cl...... R C R Cl. + . .. CH2 N N. − .. + . + . CH2 N N. H N N .. .. O deprotonation .. . C +H Cl.. + . R −C..H N N. The resulting diazoketone is decomposed via thermolysis or photosisis to release a ketocarbene and nitrogen. The ketocarbene adds to an olefin to produce a cyclopropane, undergoes insertion into a C– H bond, or rearranges into a ketene (Wolff rearrangement). Among these subsequent processes, the following scheme shows a Wolff rearrangement.

Ybegin{XyMcompd}(900,400)(100,150){}{} Yput(0,0){YDtrigonal{0==C;1D==YlonepairB[14]{O};3==R;% 2==Yllap{$_{-}$}YlonepairA[1]{C}HYsbond N$^{+}$YtbondYlonepairA[2]{N}}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% 32 FUJITA Shinsaku: XΥMTEX

(700,160)(750,250)(830,200)% Yend{XyMcompd} Yreactrarrow{0pt}{2cm}{$YDelta$ or $hYnu$}{Ystrut} Ybegin{XyMcompd}(400,400)(100,150){}{} Yput(0,0){YDtrigonal{0==C;1D==YlonepairB[14]{O};3==R;2==YlonepairA[1]{C}H}} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (180,200)(350,80)(520,100)% Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{<-}% (400,220)(480,320)(510,200)% Yend{XyMcompd} + YlonepairA[4]{N}YtbondYlonepairA[2]{N}Yquad Yreactrarrow{0pt}{3cm}{Wolff}{Rearrangement} Ybegin{XyMcompd}(500,400)(-100,100){}{} YRtrigonal{0==C;2==R;3==H;1D==YlonepairA[34]{O}Ydbond C} Yend{XyMcompd} ...... H O O Δ hν or . . Wolﬀ . +.N N. .O.. C C C C Rearrangement .. + . .. R −CH N N. R CH R 3.7.2 Williamson Ether Synthesis

Williamson Ether Synthesis is a typical SN2 reaction to produce an ether by starting from an alcohol and an halide (or sulfonate).

Ybegin{XyMcompd}(1800,700)(200,300){}{} Yput(0,0){Ycyclopentanevi{1Sb==H;1Sa==YlonepairA[124]{O}$^{Y:-}$Na$^{+}$}} Yput(650,500){+} Yput(800,500){% CH$_{3}$(CH$_{2}$)$_{15}$CH$_{2}$YsbondYlonepairA[13]{O}SO$_{2}$CH$_{3}$} Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (500,900)(900,1000)(1300,900)(1400,580) Ypscurve[unit=Yunitlength,linewidth=0.4pt,linecolor=red]{->}% (1630,550)(1680,700)(1740,600)% Yend{XyMcompd} Yreactrarrow{0pt}{2cm}{DMSO}{Ystrut} Ybegin{XyMcompd}(1000,700)(200,300){}{} Yput(0,0){Ycyclopentanevi{1Sb==H;1Sa==% YlonepairA[14]{O}CH$_{2}$(CH$_{2}$)$_{15}$CH$_{3}$}} Yend{XyMcompd} Ykern-1cm + Na$^{+}$ $^{-Y:}$YlonepairA[134]{O}SO$_{2}$CH$_{3}$

....− + ... H .O. Na H .OCH2(CH2)15CH3 DMSO + −... .. +Na .O..SO2CH3 +CH3(CH2)15CH2 O..SO2CH3 Bibliography

[1] Fujita S., “Typesetting structural formulas with the text formatter TEX/LATEX”, Comput. Chem., 18, 109 (1994).

[2] Fujita S., “XΥMTEX for Drawing Chemical Structural Formulas”, TUGboat, 16 (1), 80 (1995). [3] Fujita, S., XΥMTEX—Typesetting Chemical Structural Formulas, Addison-Wesley, Tokyo (1997). The book title is abbreviated as “XΥMTEXbook” in the present manual. [4] Fujita, S., Tanaka, N., “XΥM Notation for Electronic Communication of Organic Chemical Struc- tures”, J.Chem.Inf.Comput.Sci., 39, 903 (1999).

[5] Fujita, S., Tanaka, N., “XΥMTEX (Version 2.00) as Implementation of the XΥM Notation and the XΥM Markup Language”, TUGboat, 21 (1), 7 (2000). [6] Fujita, S., Tanaka, N., TUGboat, 22 (4), 285 (2001).

[7] Fujita, S., “XΥMTEX (Version 4.01) for Typesetting Chemical Structural Formulas. A Tool for DVI- and PostScript-Typsetting”, On-line manual (2004).

[8] Fujita, S., “XΥMTEX (Version 4.02, 4.03) for Typesetting Chemical Structural Formulas. An Exten- sion for Stereochemistry According to PostScript”, On-line manual (2004, 2005).

[9] Fujita, S., “XΥMTEX (Version 4.04) for Typesetting Chemical Structural Formulas. An Extension for Drawing Steroid Derivatives”, On-line manual (2009).

[10] Schmidt, W., “Using Common PostScript fonts with LATEX”, On-line manual for Version 9.2: http://ctan.org/tex-archive/macros/latex/required/psnfss/psnfss2e.pdf

[11] For graphic applications of TEX, LATEX and relevant systems, see Goossens, M., Mittelbach, F., Rahtz, S., Roegel, D., Voß, H., The LATEX Graphics Companion, 2nd Ed., Addison Wesley, Upper Saddle River (2008).

[12] Fujita, S., LATEX2ε Kaitei, 3rd Ed., Volumes I and II, Pearson Educ. Japan, Tokyo (2009). [13] van Zandt, T., Girou, D., “Inside PSTricks”, TUGboat, 15 (3), 239 (1995).

[14] Fujita, S., Kagakusha, Seikagakusha no tame no LATEX (LATEX for Organic Chemists and Bio- chemists), Tokyo Kagaku Dojin, Tokyo (1993).